Buggy code:
@ InventoryContainer public class ContainerAlternateGui extends Container { private EntityPlayer player ; private InventoryAlternateGui inventory ; private int xSize = 0 ; private int ySize = 0 ; private ItemStack stack ; private int filterAdvSlotIdStart ; private ArrayList < ItemStack > upgrades ; public ContainerAlternateGui ( InventoryAlternateGui inventoryAlternateGui , int xSize , int ySize ) { } public ContainerAlternateGui ( InventoryAlternateGui inventoryAlternateGui ) { } public EntityPlayer getPlayer ( ) { } public InventoryAlternateGui getInventoryAlternateGui ( ) { } public ItemStack getStack ( ) { } public int getFilterAdvSlotIdStart ( ) { } private void layoutContainer ( IInventory playerInventory , IInventory customInv , int xSize , int ySize ) { ItemStack baseBackpack = IronBackpacksHelper . getBackpack ( player ) ; ArrayList < ItemStack > upgrades = IronBackpacksHelper . getUpgradesAppliedFromNBT ( baseBackpack ) ; int advFilterRow = ( UpgradeMethods . hasFilterAdvancedUpgrade ( upgrades ) ) ? 0 : - 1 ; if ( UpgradeMethods . hasFilterBasicUpgrade ( upgrades ) ) advFilterRow ++ ; if ( UpgradeMethods . hasFilterFuzzyUpgrade ( upgrades ) ) advFilterRow ++ ; if ( UpgradeMethods . hasFilterOreDictUpgrade ( upgrades ) ) advFilterRow ++ ; if ( UpgradeMethods . hasFilterModSpecificUpgrade ( upgrades ) ) advFilterRow ++ ; filterAdvSlotIdStart = advFilterRow * 9 ; int rowCount = ( ( int ) ( Math . floor ( ( ( customInv . getSizeInventory ( ) ) // 9 ) ) ) ) ; int colCount = 9 ; <START_BUG> int yStart = ( UpgradeMethods . hasRenamingUpgrade ( upgrades ) ) ? 18 : 0 ; <END_BUG> for ( int row = 0 ; row < rowCount ; row ++ ) { yStart += 36 ; for ( int col = 0 ; col < colCount ; col ++ ) { addSlotToContainer ( new gr8pefish . ironbackpacks . container . slot . GhostSlot ( customInv , ( col + ( row * colCount ) ) , ( 20 + ( col * 18 ) ) , yStart ) ) ; } } int leftCol = ( ( xSize - 162 ) // 2 ) + 1 ; for ( int playerInvRow = 0 ; playerInvRow < 3 ; playerInvRow ++ ) { for ( int playerInvCol = 0 ; playerInvCol < 9 ; playerInvCol ++ ) { addSlotToContainer ( new net . minecraft . inventory . Slot ( playerInventory , ( ( playerInvCol + ( playerInvRow * 9 ) ) + 9 ) , ( leftCol + ( playerInvCol * 18 ) ) , ( ( ySize - ( ( 4 - playerInvRow ) * 18 ) ) - 10 ) ) ) ; } } for ( int hotbarSlot = 0 ; hotbarSlot < 9 ; hotbarSlot ++ ) { addSlotToContainer ( new net . minecraft . inventory . Slot ( playerInventory , hotbarSlot , ( leftCol + ( hotbarSlot * 18 ) ) , ( ySize - 24 ) ) ) ; } } @ Override public ItemStack transferStackInSlot ( EntityPlayer p , int i ) { } @ Override public boolean canInteractWith ( EntityPlayer player ) { } @ Override public void onContainerClosed ( EntityPlayer player ) { } @ Override public ItemStack slotClick ( int slot , int button , int flag , EntityPlayer player ) { } public void renameBackpack ( String toName ) { } public void removeSlotsInRow ( int row ) { } @ ChestContainer . RowSizeCallback public int getNumColumns ( ) { } public void initFilterSlots ( ) { } public void changeAdvFilterSlots ( String side ) { } private void saveSlots ( ) { } public int getWraparoundIndex ( int orderNumber ) { } public void setAdvFilterButtonType ( int index , int typeToSetTo ) { } }

Fix:
int yStart = ( ConfigHandler . renamingUpgradeRequired ) ? UpgradeMethods . hasRenamingUpgrade ( upgrades ) ? 18 : 0 : 18 ;